#!/bin/bash --login
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=50
#SBATCH --mem=80G
#SBATCH --job-name=salsa2
#SBATCH --time=160:00:00
#SBATCH --partition=general
#SBATCH --account=a_qaafi_genomics
#SBATCH -o juicer.slurm.out
#SBATCH -e juicer.slurm.error
#module perl
#module load salsa/2.3
/scratch/project/qaafi-cnafs/jingping/software/miniconda3/bin/bowtie2-build /scratch/project_mnt/S0030/jingping/01.Banana_genome_project/17.SALSA2/genome/genome.fa contigs -p 50
samtools faidx /scratch/project_mnt/S0030/jingping/01.Banana_genome_project/17.SALSA2/genome/genome.fa
/scratch/project/qaafi-cnafs/jingping/software/miniconda3/bin/bowtie2 -p 50 -x contigs -1 fastq/HiC_R1.fastq.gz -2 fastq/HiC_R2.fastq.gz | samtools view -S -b > align.bam
/scratch/project/qaafi-cnafs/jingping/software/miniconda3/bin/bamToBed -i align.bam > align.bed
module load salsa2/2.3
run_pipeline.py -a /scratch/project_mnt/S0030/jingping/01.Banana_genome_project/17.SALSA2/genome/genome.fa -l /scratch/project_mnt/S0030/jingping/01.Banana_genome_project/17.SALSA2/genome/genome.fa.fai -b align.bed -o test_salsaout -e TTAA,GTAC --clean yes --exp 877
